I am trying to script some of this setup, and I am trying to use the WebAdministration powershell module, and am looking at AppCmd, but when I try to set a Default Document setting this way, the setting gets added to Web.Config... and since the websites have a shared document root, they all share the same Web.Config, and this causes a problem.

Is there a way when using WebAdministration or AppCmd to specify that I want the change made specifically in applicationHost.config, not Web.config?